Index

_

__init__() (in module NeuroRuler.GUI.helpers.ErrorMessageBox) (in module NeuroRuler.GUI.main.MainWindow) (NeuroRuler.GUI.helpers.ErrorMessageBox method) (NeuroRuler.GUI.helpers.InformationDialog method) (NeuroRuler.GUI.main.MainWindow method) (NeuroRuler.utils.exceptions.ArraysDifferentShape method) (NeuroRuler.utils.exceptions.ComputeCircumferenceOfInvalidSlice method) (NeuroRuler.utils.exceptions.InvalidColor method) (NeuroRuler.utils.exceptions.InvalidJSONField method) (NeuroRuler.utils.exceptions.RotationOutOfBounds method)

A

are_properties_eq() (in module NeuroRuler.utils.img_helpers)

ArraysDifferentShape

B

background_color_of_binary_thresholded_slice() (in module NeuroRuler.utils.imgproc) Binary (NeuroRuler.utils.constants.ThresholdFilter attribute) BINARY_THRESHOLD_FILTER (in module NeuroRuler.utils.global_vars)

BinaryColor (class in NeuroRuler.utils.constants) Black (NeuroRuler.utils.constants.BinaryColor attribute) browse_files() (NeuroRuler.GUI.main.MainWindow method)

C

center (NeuroRuler.utils.img_helpers.ImageProperties attribute) clear_globals() (in module NeuroRuler.utils.img_helpers) cli() (in module NeuroRuler.CLI) ComputeCircumferenceOfInvalidSlice

CONDUCTANCE_PARAMETER (in module NeuroRuler.utils.cli_settings) (in module NeuroRuler.utils.global_vars) contour() (in module NeuroRuler.utils.imgproc), [1] CONTOUR_COLOR (in module NeuroRuler.utils.gui_settings) CURR_IMAGE_INDEX (in module NeuroRuler.utils.global_vars)

D

DEBUG (in module NeuroRuler.utils.cli_settings) (in module NeuroRuler.utils.gui_settings) degrees_to_radians() (in module NeuroRuler.utils.constants) del_curr_img() (in module NeuroRuler.utils.img_helpers) deprecated() (in module NeuroRuler.utils.constants), [1] disable_binary_threshold_inputs() (NeuroRuler.GUI.main.MainWindow method) disable_elements() (NeuroRuler.GUI.main.MainWindow method)

DISPLAY_ADVANCED_MENU_MESSAGES_IN_TERMINAL (in module NeuroRuler.utils.gui_settings) display_dimensions() (in module NeuroRuler.GUI.main) display_direction() (in module NeuroRuler.GUI.main) display_metadata() (in module NeuroRuler.GUI.main) display_properties() (in module NeuroRuler.GUI.main) display_spacing() (in module NeuroRuler.GUI.main) distance_2d_with_spacing() (in module NeuroRuler.utils.imgproc)

E

enable_binary_threshold_inputs() (NeuroRuler.GUI.main.MainWindow method) enable_elements() (NeuroRuler.GUI.main.MainWindow method) error_message_box() (in module NeuroRuler.GUI.main)

ErrorMessageBox (class in NeuroRuler.GUI.helpers) EULER_3D_TRANSFORM (in module NeuroRuler.utils.global_vars) export_curr_slice_as_img() (NeuroRuler.GUI.main.MainWindow method) export_json() (NeuroRuler.GUI.main.MainWindow method)

F

FILE (in module NeuroRuler.utils.cli_settings)

FILE_BROWSER_START_DIR (in module NeuroRuler.utils.gui_settings)

G

get_all_paths() (in module NeuroRuler.utils.img_helpers) get_center_of_rotation() (in module NeuroRuler.utils.img_helpers) get_curr_binary_thresholded_slice() (in module NeuroRuler.utils.img_helpers) get_curr_image() (in module NeuroRuler.utils.img_helpers) get_curr_image_size() (in module NeuroRuler.utils.img_helpers) get_curr_metadata() (in module NeuroRuler.utils.img_helpers) get_curr_otsu_slice() (in module NeuroRuler.utils.img_helpers) get_curr_path() (in module NeuroRuler.utils.img_helpers) get_curr_physical_units() (in module NeuroRuler.utils.img_helpers) get_curr_properties_tuple() (in module NeuroRuler.utils.img_helpers)

get_curr_rotated_slice() (in module NeuroRuler.utils.img_helpers), [1] get_curr_smooth_slice() (in module NeuroRuler.utils.img_helpers) get_middle_dimension() (in module NeuroRuler.utils.img_helpers) get_path_stem() (in module NeuroRuler.utils.constants) get_properties_from_path() (in module NeuroRuler.utils.img_helpers) get_properties_from_sitk_image() (in module NeuroRuler.utils.img_helpers) get_rotated_slice_hardcoded() (in module NeuroRuler.utils.img_helpers) get_settings() (in module NeuroRuler.utils.cli_settings) GROUP_MAX_SPACING_DIFF (in module NeuroRuler.utils.global_vars) (in module NeuroRuler.utils.gui_settings) gui() (in module NeuroRuler.GUI)

I

IMAGE_DICT (in module NeuroRuler.utils.global_vars) image_dict_is_empty() (in module NeuroRuler.utils.img_helpers) ImageProperties (class in NeuroRuler.utils.img_helpers) import_json() (NeuroRuler.GUI.main.MainWindow method) information_dialog() (in module NeuroRuler.GUI.main)

InformationDialog (class in NeuroRuler.GUI.helpers) InformationMessageBox() (in module NeuroRuler.GUI.helpers) initialize_globals() (in module NeuroRuler.utils.img_helpers) InvalidColor InvalidJSONField iterable_of_str_to_str() (in module NeuroRuler.utils.parser)

J

JSON_CLI_CONFIG_PATH (in module NeuroRuler.utils.constants)

JSON_GUI_CONFIG_PATH (in module NeuroRuler.utils.constants) JSON_SETTINGS (in module NeuroRuler.utils.parser)

L

length_of_contour() (in module NeuroRuler.utils.imgproc), [1] length_of_contour_with_spacing() (in module NeuroRuler.utils.imgproc)

load_json() (in module NeuroRuler.utils.parser) LOWER_BINARY_THRESHOLD (in module NeuroRuler.utils.cli_settings) (in module NeuroRuler.utils.global_vars)

M

main() (in module NeuroRuler.CLI.main) (in module NeuroRuler.GUI.main) MainWindow (class in NeuroRuler.GUI.main) mask_QImage() (in module NeuroRuler.GUI.helpers) MAX_NUM_MISMATCHED_PIXELS_FOR_BACKGROUND_COLOR_DETECTION (in module NeuroRuler.utils.imgproc) MESSAGE_TO_SHOW_IF_UNITS_NOT_FOUND (in module NeuroRuler.utils.constants) module NeuroRuler NeuroRuler.CLI NeuroRuler.CLI.main NeuroRuler.GUI NeuroRuler.GUI.helpers NeuroRuler.GUI.main NeuroRuler.utils NeuroRuler.utils.cli_settings NeuroRuler.utils.constants NeuroRuler.utils.exceptions NeuroRuler.utils.global_vars NeuroRuler.utils.gui_settings NeuroRuler.utils.img_helpers NeuroRuler.utils.imgproc NeuroRuler.utils.parser

N

NeuroRuler module NeuroRuler.CLI module NeuroRuler.CLI.main module NeuroRuler.GUI module NeuroRuler.GUI.helpers module NeuroRuler.GUI.main module NeuroRuler.utils module NeuroRuler.utils.cli_settings module NeuroRuler.utils.constants module

NeuroRuler.utils.exceptions module NeuroRuler.utils.global_vars module NeuroRuler.utils.gui_settings module NeuroRuler.utils.img_helpers module NeuroRuler.utils.imgproc module NeuroRuler.utils.parser module next_img() (in module NeuroRuler.utils.img_helpers) (NeuroRuler.GUI.main.MainWindow method) NIFTI_METADATA_UNITS_KEY (in module NeuroRuler.utils.constants) NIFTI_METADATA_UNITS_VALUE_TO_PHYSICAL_UNITS (in module NeuroRuler.utils.constants) NUM_CONTOURS_IN_INVALID_SLICE (in module NeuroRuler.utils.constants) NUM_DIGITS_TO_ROUND_TO (in module NeuroRuler.utils.constants) NUM_PIXELS_TO_CHECK_ON_EACH_EDGE_FOR_BACKGROUND_COLOR_DETECTION (in module NeuroRuler.utils.imgproc)

O

orient_curr_image() (in module NeuroRuler.utils.img_helpers) (NeuroRuler.GUI.main.MainWindow method) ORIENT_FILTER (in module NeuroRuler.utils.global_vars)

ORIENTATION_STRINGS (in module NeuroRuler.utils.constants) Otsu (NeuroRuler.utils.constants.ThresholdFilter attribute) OTSU_THRESHOLD_FILTER (in module NeuroRuler.utils.global_vars) OUTPUT_DIR (in module NeuroRuler.utils.constants)

P

parse_bool() (in module NeuroRuler.utils.parser) parse_cli() (in module NeuroRuler.utils.parser) parse_cli_config() (in module NeuroRuler.utils.parser) parse_float() (in module NeuroRuler.utils.parser) parse_gui_cli() (in module NeuroRuler.utils.parser), [1] parse_gui_config() (in module NeuroRuler.utils.parser)

parse_int() (in module NeuroRuler.utils.parser) parse_main_color_from_theme_json() (in module NeuroRuler.utils.parser) parse_path() (in module NeuroRuler.utils.parser) parse_str() (in module NeuroRuler.utils.parser) previous_img() (in module NeuroRuler.utils.img_helpers) (NeuroRuler.GUI.main.MainWindow method) PRIMARY_MONITOR_DIMENSIONS (in module NeuroRuler.utils.constants)

R

RAW (in module NeuroRuler.utils.cli_settings) READER (in module NeuroRuler.utils.global_vars) remove_curr_img() (NeuroRuler.GUI.main.MainWindow method) render_all_sliders() (NeuroRuler.GUI.main.MainWindow method) render_circumference() (NeuroRuler.GUI.main.MainWindow method) render_curr_slice() (in module NeuroRuler.GUI.main.MainWindow), [1] (NeuroRuler.GUI.main.MainWindow method) render_image_num_and_path() (NeuroRuler.GUI.main.MainWindow method) render_scaled_qpixmap_from_qimage() (NeuroRuler.GUI.main.MainWindow method) render_smooth_slice() (NeuroRuler.GUI.main.MainWindow method)

render_threshold() (NeuroRuler.GUI.main.MainWindow method) reset_settings() (NeuroRuler.GUI.main.MainWindow method) resizeEvent() (NeuroRuler.GUI.main.MainWindow method) rotate_x() (in module NeuroRuler.GUI.main.MainWindow) (NeuroRuler.GUI.main.MainWindow method) rotate_y() (NeuroRuler.GUI.main.MainWindow method) rotate_z() (NeuroRuler.GUI.main.MainWindow method) ROTATION_MAX (in module NeuroRuler.utils.constants) ROTATION_MIN (in module NeuroRuler.utils.constants) RotationOutOfBounds

S

select_largest_component() (in module NeuroRuler.utils.imgproc) set_curr_image() (in module NeuroRuler.utils.img_helpers) set_view_z() (NeuroRuler.GUI.main.MainWindow method) settings_export_view_toggle() (NeuroRuler.GUI.main.MainWindow method) SETTINGS_VIEW_ENABLED (in module NeuroRuler.GUI.main) sitk_slice_to_qimage() (in module NeuroRuler.GUI.helpers) size (NeuroRuler.utils.img_helpers.ImageProperties attribute) SLICE (in module NeuroRuler.utils.cli_settings) (in module NeuroRuler.utils.global_vars)

slice_update() (NeuroRuler.GUI.main.MainWindow method) SMOOTHING_FILTER (in module NeuroRuler.utils.global_vars) SMOOTHING_ITERATIONS (in module NeuroRuler.utils.cli_settings) (in module NeuroRuler.utils.global_vars) spacing (NeuroRuler.utils.img_helpers.ImageProperties attribute) STARTUP_HEIGHT_RATIO (in module NeuroRuler.utils.gui_settings) STARTUP_WIDTH_RATIO (in module NeuroRuler.utils.gui_settings) string_to_QColor() (in module NeuroRuler.GUI.helpers) SUPPORTED_IMAGE_EXTENSIONS (in module NeuroRuler.utils.constants) SUPPORTED_IMAGE_EXTENSIONS_REGEX (in module NeuroRuler.utils.constants)

T

test_stuff() (NeuroRuler.GUI.main.MainWindow method) THEME_DIR (in module NeuroRuler.utils.constants) THEME_NAME (in module NeuroRuler.utils.gui_settings) THEMES (in module NeuroRuler.utils.constants) THETA_X (in module NeuroRuler.utils.cli_settings) (in module NeuroRuler.utils.global_vars) THETA_Y (in module NeuroRuler.utils.cli_settings) (in module NeuroRuler.utils.global_vars)

THETA_Z (in module NeuroRuler.utils.cli_settings) (in module NeuroRuler.utils.global_vars) THRESHOLD_FILTER (in module NeuroRuler.utils.cli_settings) ThresholdFilter (class in NeuroRuler.utils.constants) TIME_STEP (in module NeuroRuler.utils.cli_settings) (in module NeuroRuler.utils.global_vars) toggle_setting_to_false() (NeuroRuler.GUI.main.MainWindow method) toggle_setting_to_true() (NeuroRuler.GUI.main.MainWindow method)

U

UNSCALED_QPIXMAP (in module NeuroRuler.GUI.main) update_binary_filter_settings() (NeuroRuler.GUI.main.MainWindow method) update_images() (in module NeuroRuler.utils.img_helpers)

update_smoothing_settings() (NeuroRuler.GUI.main.MainWindow method) update_view() (NeuroRuler.GUI.main.MainWindow method) UPPER_BINARY_THRESHOLD (in module NeuroRuler.utils.cli_settings) (in module NeuroRuler.utils.global_vars)

V

View (class in NeuroRuler.utils.constants)

VIEW (in module NeuroRuler.utils.global_vars)

W

White (NeuroRuler.utils.constants.BinaryColor attribute)

WINDOW_TITLE_PADDING (in module NeuroRuler.GUI.helpers)

X

X (NeuroRuler.utils.constants.View attribute)

X_CENTER (in module NeuroRuler.utils.global_vars) X_ORIENTATION_STR (in module NeuroRuler.utils.constants)

Y

Y (NeuroRuler.utils.constants.View attribute)

Y_CENTER (in module NeuroRuler.utils.global_vars) Y_ORIENTATION_STR (in module NeuroRuler.utils.constants)

Z

Z (NeuroRuler.utils.constants.View attribute)

Z_ORIENTATION_STR (in module NeuroRuler.utils.constants)